library(png)
## First consolidate the available files into a single table
path <- "~/Box Sync/Four model compare/Module 2"
setwd(path)
myfiles_full <- list.dirs()
analyze_this_many <- length(myfiles_full)
available_files <- matrix(NA, 1, 1)
for(i in 1: analyze_this_many){
available_files <- rbind(available_files , as.matrix(list.files(myfiles_full[i], full.names = TRUE)))
}
dim(available_files)
split.file.name <- strsplit(available_files[10], split = "_")
available <- list.files()
files <- matrix(rep(NA, 62), length(available), 62)
dim(files)
i <- 10
for(i in 1:length(available)){
load(available[i])
name <- unlist(strsplit(available[i], split="_"))
files[i,] <- c(as.vector(matrix(name, 1,35)),matrix(Sim_statistics[[1]], 1, 27))
}
colnames(files) <- c(
NA,
"background_takeover_type" ,
NA,
"replicate",
NA,
"Model_type",
rep(NA,2),
"speciation_of_Env_NonD",
"speciation_of_Env_D",
"speciation_of_For",
"speciation_of_Dom",
NA,
"extinction_of_Env_NonD",
"extinction_of_Env_D",
"extinction_of_For",
"extinction_of_Dom",
NA,
"P.diffusion_Target_forager",
"P.diffusion_Target_domesticator",
"P.diffusion_Source_forager",
"P.diffusion_Source_domesticator",
NA,
"P.takeover_Target_forager",
"P.takeover_Target_domesticator",
"P.takeover_Source_forager",
"P.takeover_Source_domesticator",
NA,
"arisal_of_Env_NonD",
"arisal_of_Env_D",
"arisal_of_For",
"arisal_of_Dom",
NA,
"timesteps",
NA,
"number_of_branches",
"Pylo_diversity_is_sum_of_BL",
"average_phylogenetic_diversity_is_mean_of_BL",
"variance_Pylo_diversity_is_variance_of_BL",
"F_quadratic_entropy_is_sum_of_PD",
"Mean_pairwise_distance",
"variance_pairwise_distance",
"Evolutionary_distinctiveness_sum",
"mean_Phylogenetic_isolation",
"variance_Phylogenetic_isolation",
"gamma",
"gamma_p_value",
"speciation_rate",
"extinction_rate",
"extinction_per_speciation",
"speciation_minus_extinction",
"trait_1_speciation",
"trait_2_speciation" ,
"trait_1_extinction" ,
"trait_2_extinction" ,
"transition_from_trait_1_to_2" ,
"transition_from_trait_2_to_1" ,
"transition_rate_ratio_1to2_over_2to1" ,
"Phylogenetic_signal",
"spatial.tests.fora",
"spatial.tests.dom",
"prevalence"
)
results_table <- as.data.frame(files)
head(results_table)
dim(results_table)
Concatenated_data <- results_table
save(Concatenated_data, file="~/Desktop/Four_model_compare_results.Rdata")
one <- subset(results_table, Model_type=="01" )
two <- subset(results_table, Model_type=="02" )
three <- subset(results_table, Model_type=="03" )
four <- subset(results_table, Model_type=="04" )
crop <- min(length(one[,1]),
length(two[,1]),
length(three[,1]),
length(four[,1]))
one <- one[1:crop,]
two <- two[1:crop,]
three <- three[1:crop,]
four <- four[1:crop,]
Concatenated_data <- rbind(one, two, three, four)
dim(Concatenated_data)
save(Concatenated_data, file="~/Desktop/Four_model_compare_results.Rdata")
crop
## First consolidate the available files into a single table
path <- "~/Box Sync/Four model compare/Module 2 extinct"
setwd(path)
Error in setwd(path) : cannot change working directory
load('~/Box Sync/colliding ranges/Simulations_humans/Results/Four_model_compare_results_extinct.Rdata')
extinct <- Concatenated_data
load('~/Box Sync/colliding ranges/Simulations_humans/Results/Four_model_compare_results.Rdata')
extant <- Concatenated_data
names(extinct)
[1] NA
[2] "background_takeover_type"
[3] NA
[4] "replicate"
[5] NA
[6] "Model_type"
[7] NA
[8] NA
[9] "speciation_of_Env_NonD"
[10] "speciation_of_Env_D"
[11] "speciation_of_For"
[12] "speciation_of_Dom"
[13] NA
[14] "extinction_of_Env_NonD"
[15] "extinction_of_Env_D"
[16] "extinction_of_For"
[17] "extinction_of_Dom"
[18] NA
[19] "P.diffusion_Target_forager"
[20] "P.diffusion_Target_domesticator"
[21] "P.diffusion_Source_forager"
[22] "P.diffusion_Source_domesticator"
[23] NA
[24] "P.takeover_Target_forager"
[25] "P.takeover_Target_domesticator"
[26] "P.takeover_Source_forager"
[27] "P.takeover_Source_domesticator"
[28] NA
[29] "arisal_of_Env_NonD"
[30] "arisal_of_Env_D"
[31] "arisal_of_For"
[32] "arisal_of_Dom"
[33] NA
[34] "timesteps"
[35] NA
[36] "number_of_branches"
[37] "Pylo_diversity_is_sum_of_BL"
[38] "average_phylogenetic_diversity_is_mean_of_BL"
[39] "variance_Pylo_diversity_is_variance_of_BL"
[40] "F_quadratic_entropy_is_sum_of_PD"
[41] "Mean_pairwise_distance"
[42] "variance_pairwise_distance"
[43] "Evolutionary_distinctiveness_sum"
[44] "mean_Phylogenetic_isolation"
[45] "variance_Phylogenetic_isolation"
[46] "gamma"
[47] "gamma_p_value"
[48] "speciation_rate"
[49] "extinction_rate"
[50] "extinction_per_speciation"
[51] "speciation_minus_extinction"
[52] "trait_1_speciation"
[53] "trait_2_speciation"
[54] "trait_1_extinction"
[55] "trait_2_extinction"
[56] "transition_from_trait_1_to_2"
[57] "transition_from_trait_2_to_1"
[58] "transition_rate_ratio_1to2_over_2to1"
[59] "Phylogenetic_signal"
[60] "spatial.tests.fora"
[61] "spatial.tests.dom"
[62] "prevalence"
names(extant)
[1] NA
[2] "background_takeover_type"
[3] "NA.1"
[4] "replicate"
[5] "NA.2"
[6] "Model_type"
[7] "NA.3"
[8] "NA.4"
[9] "speciation_of_Env_NonD"
[10] "speciation_of_Env_D"
[11] "speciation_of_For"
[12] "speciation_of_Dom"
[13] "NA.5"
[14] "extinction_of_Env_NonD"
[15] "extinction_of_Env_D"
[16] "extinction_of_For"
[17] "extinction_of_Dom"
[18] "NA.6"
[19] "P.diffusion_Target_forager"
[20] "P.diffusion_Target_domesticator"
[21] "P.diffusion_Source_forager"
[22] "P.diffusion_Source_domesticator"
[23] "NA.7"
[24] "P.takeover_Target_forager"
[25] "P.takeover_Target_domesticator"
[26] "P.takeover_Source_forager"
[27] "P.takeover_Source_domesticator"
[28] "NA.8"
[29] "arisal_of_Env_NonD"
[30] "arisal_of_Env_D"
[31] "arisal_of_For"
[32] "arisal_of_Dom"
[33] "NA.9"
[34] "timesteps"
[35] "NA.10"
[36] "number_of_branches"
[37] "Pylo_diversity_is_sum_of_BL"
[38] "average_phylogenetic_diversity_is_mean_of_BL"
[39] "variance_Pylo_diversity_is_variance_of_BL"
[40] "F_quadratic_entropy_is_sum_of_PD"
[41] "Mean_pairwise_distance"
[42] "variance_pairwise_distance"
[43] "Evolutionary_distinctiveness_sum"
[44] "mean_Phylogenetic_isolation"
[45] "variance_Phylogenetic_isolation"
[46] "gamma"
[47] "gamma_p_value"
[48] "speciation_rate"
[49] "extinction_rate"
[50] "extinction_per_speciation"
[51] "speciation_minus_extinction"
[52] "trait_1_speciation"
[53] "trait_2_speciation"
[54] "trait_1_extinction"
[55] "trait_2_extinction"
[56] "transition_from_trait_1_to_2"
[57] "transition_from_trait_2_to_1"
[58] "transition_rate_ratio_1to2_over_2to1"
[59] "Phylogenetic_signal"
[60] "spatial.tests.fora"
[61] "spatial.tests.dom"
[62] "prevalence"
for(i in c(9,10,11,12,14,15,16,17,19,20,21,22,24,25,26,27,29,30,31,32)){
extinct[which(is.nan(as.numeric(as.character(extinct[, i]))) == TRUE), i] <- NA
}
for(i in c(9,10,11,12,14,15,16,17,19,20,21,22,24,25,26,27,29,30,31,32)){
extant[which(is.nan(as.numeric(as.character(extant[, i]))) == TRUE), i] <- NA
}
i <- 19
for(i in c(20,21,24,25,26,27)){
extinct[which(as.numeric(as.character(extinct[, i])) == 0), i] <- NA
}
for(i in c(20,21,24,25,26,27)){
extant[which(as.numeric(as.character(extant[, i])) == 0), i] <- NA
}
xlimit <- c(0,1)
ylimit <- c(0,600)
maincex <- 0.9
png(file="Global_success_rate_per_parameter.png", width=8.5, height=11, units="in", res=300)
par(mfrow=c(5,4), mar=c(3,3,3,0))
hist(as.numeric(as.character(extinct[,9])), main="speciation of F in F env", col=adjustcolor("firebrick", alpha=0.7), breaks=100, border=NA, xlim= xlimit, ylim= ylimit, cex.main= maincex)
hist(as.numeric(as.character(extant[,9])), main="speciation of F in F env", col=adjustcolor("cornflowerblue", alpha=0.7), breaks=100, border=NA, xlim= xlimit, ylim= ylimit, cex.main= maincex, add=TRUE)
hist(as.numeric(as.character(extinct[,10])), main="speciation of D in F env", col=adjustcolor("firebrick", alpha= 0.7), breaks=100, border=NA, xlim= xlimit, ylim= ylimit, cex.main= maincex)
hist(as.numeric(as.character(extant[,10])), main="speciation of D in F env", col=adjustcolor("cornflowerblue", alpha= 0.7), breaks=100, border=NA, xlim= xlimit, ylim= ylimit, cex.main= maincex, add=TRUE)
hist(as.numeric(as.character(extinct[,11])), main="speciation of F in D env", col=adjustcolor("firebrick", alpha= 0.7), breaks=100, border=NA, xlim= xlimit, ylim= ylimit, cex.main= maincex)
hist(as.numeric(as.character(extant[,11])), main="speciation of F in D env", col=adjustcolor("cornflowerblue", alpha= 0.7), breaks=100, border=NA, xlim= xlimit, ylim= ylimit, cex.main= maincex, add=TRUE)
hist(as.numeric(as.character(extinct[,12])), main="speciation of D in D env", col=adjustcolor("firebrick", alpha= 0.7), breaks=100, border=NA, xlim= xlimit, ylim= ylimit, cex.main= maincex)
hist(as.numeric(as.character(extant[,12])), main="speciation of D in D env", col=adjustcolor("cornflowerblue", alpha= 0.7), breaks=100, border=NA, xlim= xlimit, ylim= ylimit, cex.main= maincex, add=TRUE)
#######
hist(as.numeric(as.character(extinct[, 14])), main="extinction of F in F env", col=adjustcolor("firebrick", alpha= 0.7), breaks=100, border=NA, xlim= xlimit, ylim= ylimit, cex.main= maincex)
hist(as.numeric(as.character(extant[, 14])), main="extinction of F in F env", col=adjustcolor("cornflowerblue", alpha= 0.7), breaks=100, border=NA, xlim= xlimit, ylim= ylimit, cex.main= maincex, add=TRUE)
hist(as.numeric(as.character(extinct[, 15])), main="extinction of D in F env", col=adjustcolor("firebrick", alpha= 0.7), breaks=100, border=NA, xlim= xlimit, ylim= ylimit, cex.main= maincex)
hist(as.numeric(as.character(extant[, 15])), main="extinction of D in F env", col=adjustcolor("cornflowerblue", alpha= 0.7), breaks=100, border=NA, xlim= xlimit, ylim= ylimit, cex.main= maincex, add=TRUE)
hist(as.numeric(as.character(extinct[, 16])), main="extinction of F in D env", col=adjustcolor("firebrick", alpha= 0.7), breaks=100, border=NA, xlim= xlimit, ylim= ylimit, cex.main= maincex)
hist(as.numeric(as.character(extant[, 16])), main="extinction of F in D env", col=adjustcolor("cornflowerblue", alpha= 0.7), breaks=100, border=NA, xlim= xlimit, ylim= ylimit, cex.main= maincex, add=TRUE)
hist(as.numeric(as.character(extinct[, 17])), main="extinction of D in D env", col=adjustcolor("firebrick", alpha= 0.7), breaks=100, border=NA, xlim= xlimit, ylim= ylimit, cex.main= maincex)
hist(as.numeric(as.character(extant[, 17])), main="extinction of D in D env", col=adjustcolor("cornflowerblue", alpha= 0.7), breaks=100, border=NA, xlim= xlimit, ylim= ylimit, cex.main= maincex, add=TRUE)
######
hist(as.numeric(as.character(extinct[, 29])), main="arisal of F in F env", col=adjustcolor("firebrick", alpha= 0.7), breaks=100, border=NA, xlim= xlimit, ylim= ylimit, cex.main= maincex)
hist(as.numeric(as.character(extant[, 29])), main="arisal of F in F env", col=adjustcolor("cornflowerblue", alpha= 0.7), breaks=100, border=NA, xlim= xlimit, ylim= ylimit, cex.main= maincex, add=TRUE)
hist(as.numeric(as.character(extinct[, 30])), main="arisal of D in F env", col=adjustcolor("firebrick", alpha= 0.7), breaks=100, border=NA, xlim= xlimit, ylim= ylimit, cex.main= maincex)
hist(as.numeric(as.character(extant[, 30])), main="arisal of D in F env", col=adjustcolor("cornflowerblue", alpha= 0.7), breaks=100, border=NA, xlim= xlimit, ylim= ylimit, cex.main= maincex, add=TRUE)
hist(as.numeric(as.character(extinct[, 31])), main="arisal of F in D env", col=adjustcolor("firebrick", alpha= 0.7), breaks=100, border=NA, xlim= xlimit, ylim= ylimit, cex.main= maincex)
hist(as.numeric(as.character(extant[, 31])), main="arisal of F in D env", col=adjustcolor("cornflowerblue", alpha= 0.7), breaks=100, border=NA, xlim= xlimit, ylim= ylimit, cex.main= maincex, add=TRUE)
hist(as.numeric(as.character(extinct[, 32])), main="arisal of D in D env", col=adjustcolor("firebrick", alpha= 0.7), breaks=100, border=NA, xlim= xlimit, ylim= ylimit, cex.main= maincex)
hist(as.numeric(as.character(extant[, 32])), main="arisal of D in D env", col=adjustcolor("cornflowerblue", alpha= 0.7), breaks=100, border=NA, xlim= xlimit, ylim= ylimit, cex.main= maincex, add=TRUE)
######
hist(as.numeric(as.character(extinct[, 19])), main="NOPE -- Diffusion: source F, target F", col=adjustcolor("firebrick", alpha= 0.7), breaks=100, border=NA, xlim= xlimit, ylim= c(0,18000), cex.main= maincex)
hist(as.numeric(as.character(extant[, 19])), main="NOPE -- Diffusion: source F, target F", col=adjustcolor("cornflowerblue", alpha= 0.7), breaks=100, border=NA, xlim= xlimit, ylim= c(0,18000), cex.main= maincex, add=TRUE)
hist(as.numeric(as.character(extinct[, 20])), main="Diffusion: source D, target F", col=adjustcolor("firebrick", alpha= 0.7), breaks=100, border=NA, xlim= xlimit, ylim= ylimit, cex.main= maincex)
hist(as.numeric(as.character(extant[, 20])), main="Diffusion: source D, target F", col=adjustcolor("cornflowerblue", alpha= 0.7), breaks=100, border=NA, xlim= xlimit, ylim= ylimit, cex.main= maincex, add=TRUE)
hist(as.numeric(as.character(extinct[, 21])), main="Diffusion: source F, target D", col=adjustcolor("firebrick", alpha= 0.7), breaks=100, border=NA, xlim= xlimit, ylim= ylimit, cex.main= maincex)
hist(as.numeric(as.character(extant[, 21])), main="Diffusion: source F, target D", col=adjustcolor("cornflowerblue", alpha= 0.7), breaks=100, border=NA, xlim= xlimit, ylim= ylimit, cex.main= maincex, add=TRUE)
hist(as.numeric(as.character(extinct[, 22])), main="NOPE -- Diffusion: source D, target D", col=adjustcolor("firebrick", alpha= 0.7), breaks=100, border=NA, xlim= xlimit, ylim= c(0,18000), cex.main= maincex)
hist(as.numeric(as.character(extant[, 22])), main="NOPE -- Diffusion: source D, target D", col=adjustcolor("cornflowerblue", alpha= 0.7), breaks=100, border=NA, xlim= xlimit, ylim= c(0,18000), cex.main= maincex, add=TRUE)
####
hist(as.numeric(as.character(extinct[, 24])), main="Takeover: source F, target F", col=adjustcolor("firebrick", alpha= 0.7), breaks=100, border=NA, xlim= xlimit, ylim= ylimit, cex.main= maincex)
hist(as.numeric(as.character(extant[, 24])), main="Takeover: source F, target F", col=adjustcolor("cornflowerblue", alpha= 0.7), breaks=100, border=NA, xlim= xlimit, ylim= ylimit, cex.main= maincex, add=TRUE)
hist(as.numeric(as.character(extinct[, 25])), main="Takeover: source D, target F", col=adjustcolor("firebrick", alpha= 0.7), breaks=100, border=NA, xlim= xlimit, ylim= ylimit, cex.main= maincex)
hist(as.numeric(as.character(extant[, 25])), main="Takeover: source D, target F", col=adjustcolor("cornflowerblue", alpha= 0.7), breaks=100, border=NA, xlim= xlimit, ylim= ylimit, cex.main= maincex, add=TRUE)
hist(as.numeric(as.character(extinct[, 26])), main="Takeover: source F, target D", col=adjustcolor("firebrick", alpha= 0.7), breaks=100, border=NA, xlim= xlimit, ylim= ylimit, cex.main= maincex)
hist(as.numeric(as.character(extant[, 26])), main="Takeover: source F, target D", col=adjustcolor("cornflowerblue", alpha= 0.7), breaks=100, border=NA, xlim= xlimit, ylim= ylimit, cex.main= maincex, add=TRUE)
hist(as.numeric(as.character(extinct[, 27])), main="Takeover: source D, target D", col=adjustcolor("firebrick", alpha= 0.7), breaks=100, border=NA, xlim= xlimit, ylim= ylimit, cex.main= maincex)
hist(as.numeric(as.character(extant[, 27])), main="Takeover: source D, target D", col=adjustcolor("cornflowerblue", alpha= 0.7), breaks=100, border=NA, xlim= xlimit, ylim= ylimit, cex.main= maincex, add=TRUE)
dev.off()
null device
1
png(file="extiction minus extant per outcome.png", width=8.5, height=11, units="in", res=300)
par(mfrow=c(3,1))
plot(as.numeric(as.character(extinct[,9])), as.numeric(as.character(extinct[,14])), xlab="speciation", ylab="extinction", col= adjustcolor("firebrick", alpha=0.2), pch=19, cex=0.6, ylim=c(0,1))
plot(as.numeric(as.character(extant[,9])), as.numeric(as.character(extant[,14])), xlab="speciation", ylab="extinction", col= adjustcolor("cornflowerblue", alpha=0.2), pch=19, cex=0.6, ylim=c(0,1))
plot(as.numeric(as.character(extinct[,9])), as.numeric(as.character(extinct[,14])), xlab="speciation", ylab="extinction", col= adjustcolor("firebrick", alpha=0.2), pch=19, cex=0.6, ylim=c(0,1))
points(as.numeric(as.character(extant[,9])), as.numeric(as.character(extant[,14])), xlab="speciation", ylab="extinction", col= adjustcolor("cornflowerblue", alpha=0.2), pch=19, cex=0.6)
dev.off()
null device
1
load('~/Box Sync/colliding ranges/Simulations_humans/Available trees/real.analysis.RData')
#Concatenated_data <- Concatenated_data[Concatenated_data[, 2] == "stats.no.bTO", ]
#Concatenated_data <- Concatenated_data[Concatenated_data[, 6] != "05", ]
# Concatenated_data[, 6] <- as.numeric(Concatenated_data[, 6])
# # Concatenated_data[original[, 2] == "background_takeover", 6] <- Concatenated_data[original[, 2] == "background_takeover", 6] + 4
Concatenated_data[, 6] <- factor(Concatenated_data[, 6])
head(Concatenated_data)